It means there's missing data in your dataset. Mess around with the --missingDataColor flag. See documentation:

If –missingDataAsZero was not set, such cases will be colored in black by default. Using this parameter, a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). For a list of possible color names see: http://packages.python.org/ete2/reference/reference_svgcolors.html. Other colors can be specified using the #rrggbb notation.